/project/ldv/Software/executor-venv-toil9/lib/python3.9/site-packages/pydantic/_internal/_generate_schema.py:2249: UnsupportedFieldAttributeWarning: The 'default' attribute with value None was provided to the `Field()` function, which has no effect in the context it was used. 'default' is field-specific metadata, and can only be attached to a model field using `Annotated` metadata or by assignment. This may have happened because an `Annotated` type alias using the `type` statement was used, or if the `Field()` function was attached to a single member of a union type.
warnings.warn(
Already cached git.astron.nl:5000/ldv/bf_double_tgz:latest with Singularity.
INFO:cwl_utils.image_puller:Already cached git.astron.nl:5000/ldv/bf_double_tgz:latest with Singularity.
Already cached git.astron.nl:5000/ldv/bf_double_tgz:v0.5.7 with Singularity.
INFO:cwl_utils.image_puller:Already cached git.astron.nl:5000/ldv/bf_double_tgz:v0.5.7 with Singularity.
Already cached git.astron.nl:5000/ldv/bf_double_tgz:v0.5.7 with Singularity.
INFO:cwl_utils.image_puller:Already cached git.astron.nl:5000/ldv/bf_double_tgz:v0.5.7 with Singularity.
[2026-05-13T19:33:20+0200] [MainThread] [I] [toil.lib.history] Recording workflow creation of a2cb2d71-69de-45b5-b075-5ab5b65bfde7 in file:/project/ldv/Share/cache/tmp/tmppm_96yzg
[2026-05-13T19:33:20+0200] [MainThread] [I] [toil.cwl.cwltoil] Importing input files...
[2026-05-13T19:33:20+0200] [MainThread] [I] [toil.cwl.cwltoil] Importing tool-associated files...
[2026-05-13T19:33:20+0200] [MainThread] [I] [toil.cwl.cwltoil] Starting workflow
[2026-05-13T19:33:20+0200] [MainThread] [I] [toil.lib.history] Workflow a2cb2d71-69de-45b5-b075-5ab5b65bfde7 is a run of /project/ldv/Share/run-test/workflows/psrfits_requantisation/workflow/download_and_run_psrfits_requantisation.cwl
[2026-05-13T19:33:20+0200] [MainThread] [I] [toil] Running Toil version 9.1.2-355b72ba0e425619c0367562caf2a337078dba65 on host wn-la-12.spider.surfsara.nl.
[2026-05-13T19:33:20+0200] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging.
[2026-05-13T19:33:22+0200] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run
[2026-05-13T19:33:25+0200] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_psrfits_requantisation.cwl.0.fetchdata kind-CWLJob/instance-qpudgzez v1 with job batch system ID: 3 and disk: 1.0 Gi, memory: 256.0 Mi, cores: 1, accelerators: [], preemptible: False
[2026-05-13T19:34:48+0200] [Thread-12] [I] [toil.statsAndLogging] Got message from job at time 05-13-2026 19:34:48: CWL step complete: download_and_run_psrfits_requantisation.cwl.0.fetchdata
[2026-05-13T19:34:48+0200] [Thread-12] [I] [toil.statsAndLogging] download_and_run_psrfits_requantisation.cwl.0.fetchdata.stdout follows:
=========>
Downloading /project/ldv/Share/run-test/datamanager/268599/L427020_SAP000_B000_S2_P014_bf_8800b1a8.tar to L427020_SAP000_B000_S2_P014_bf_8800b1a8.tar
<=========
[2026-05-13T19:34:51+0200] [MainThread] [I] [toil.leader] Issued job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-f7jiprcw v1 with job batch system ID: 6 and disk: 1.0 Gi, memory: 256.0 Mi, cores: 1, accelerators: [], preemptible: False
[2026-05-13T19:36:22+0200] [Thread-9] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker CWLJob /project/ldv/Share/cache/tmp/tmppm_96yzg kind-CWLJob/instance-f7jiprcw.
[2026-05-13T19:36:22+0200] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-f7jiprcw v1
Exit reason: None
[2026-05-13T19:36:22+0200] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-f7jiprcw v2
[2026-05-13T19:36:22+0200] [MainThread] [W] [toil.leader] Log from job "kind-CWLJob/instance-f7jiprcw" follows:
=========>
[2026-05-13T19:34:52+0200] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
[2026-05-13T19:34:52+0200] [MainThread] [I] [toil] Running Toil version 9.1.2-355b72ba0e425619c0367562caf2a337078dba65 on host wn-la-12.spider.surfsara.nl.
[2026-05-13T19:34:52+0200] [MainThread] [I] [toil.worker] Working on job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-f7jiprcw v1
/project/ldv/Software/executor-venv-toil9/lib/python3.9/site-packages/pydantic/_internal/_generate_schema.py:2249: UnsupportedFieldAttributeWarning: The 'default' attribute with value None was provided to the `Field()` function, which has no effect in the context it was used. 'default' is field-specific metadata, and can only be attached to a model field using `Annotated` metadata or by assignment. This may have happened because an `Annotated` type alias using the `type` statement was used, or if the `Field()` function was attached to a single member of a union type.
warnings.warn(
[2026-05-13T19:34:53+0200] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-f7jiprcw v1) from description 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-f7jiprcw v1
[2026-05-13T19:35:30+0200] [MainThread] [W] [cwltool] You have specified '--preserve-entire-environment' while running a container which will override variables set in the container. This may break the container, be non-portable, and/or affect reproducibility.
[2026-05-13T19:35:30+0200] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run-test/workflows/psrfits_requantisation/workflow
[2026-05-13T19:36:21+0200] [MainThread] [I] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] /project/ldv/Share/cache/tmp/tmpje0gk2vl$ singularity \
--quiet \
run \
--contain \
--ipc \
--cleanenv \
--no-eval \
--userns \
--home \
/project/ldv/Share/cache/tmp/tmpje0gk2vl:/nvTPZs \
--mount=type=bind,source=/tmp/tmpzu7kbutl,target=/tmp \
--pwd \
/nvTPZs \
--net \
--network \
none \
/project/ldv/Share/run-test/workflows/psrfits_requantisation/workflow/git.astron.nl:5000_ldv_bf_double_tgz:latest.sif \
psrfits_requantisation \
L427020_SAP000_B000_S2_P014_bf.tar \
--output-sasid=102600000356
[2026-05-13T19:36:21+0200] [MainThread] [W] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] exited with status: 2
[2026-05-13T19:36:21+0200] [MainThread] [E] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] Job error:
("Error collecting output for parameter 'bf_archive': ../../../../workflows/psrfits_requantisation/steps/requantize.cwl:31:5: Did not find output file with glob pattern: ['102600000356_*.tar'].", {})
[2026-05-13T19:36:21+0200] [MainThread] [W] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] completed permanentFail
[2026-05-13T19:36:21+0200] [MainThread] [E] [toil.cwl.cwltoil] Failed command standard error:
source: /.inject-apptainer-env.sh:79:11: invalid var name
Usage: psrfits_requantisation [options] [output tarball]
psrfits_requantisation: error: no such option: --output-sasid
[2026-05-13T19:36:21+0200] [MainThread] [C] [toil.worker] Worker crashed with traceback:
Traceback (most recent call last):
File "/project/ldv/Software/executor-venv-toil9/lib/python3.9/site-packages/toil/worker.py", line 595, in workerScript
job._runner(
File "/project/ldv/Software/executor-venv-toil9/lib/python3.9/site-packages/toil/job.py", line 3254, in _runner
returnValues = self._run(jobGraph=None, fileStore=fileStore)
File "/project/ldv/Software/executor-venv-toil9/lib/python3.9/site-packages/toil/job.py", line 3137, in _run
return self.run(fileStore)
File "/project/ldv/Software/executor-venv-toil9/lib/python3.9/site-packages/toil/cwl/cwltoil.py", line 2847, in run
raise cwl_utils.errors.WorkflowException(status)
cwl_utils.errors.WorkflowException: permanentFail
[2026-05-13T19:36:21+0200] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host wn-la-12.spider.surfsara.nl
<=========
[2026-05-13T19:36:22+0200] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-f7jiprcw v2 with ID kind-CWLJob/instance-f7jiprcw to 3
[2026-05-13T19:36:22+0200] [MainThread] [W] [toil.job] We have increased the default memory of the failed job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-f7jiprcw v2 to 2147483648 bytes
[2026-05-13T19:36:22+0200] [MainThread] [W] [toil.job] We have increased the disk of the failed job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-f7jiprcw v2 to the default of 2147483648 bytes
[2026-05-13T19:36:22+0200] [MainThread] [I] [toil.leader] Issued job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-f7jiprcw v3 with job batch system ID: 7 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
[2026-05-13T19:36:22+0200] [Thread-12] [I] [toil.statsAndLogging] psrfits_requantisation.cwl.requantise.requantize.cwl.stderr follows:
=========>
source: /.inject-apptainer-env.sh:79:11: invalid var name
Usage: psrfits_requantisation [options] [output tarball]
psrfits_requantisation: error: no such option: --output-sasid
<=========
[2026-05-13T19:37:12+0200] [Thread-12] [I] [toil.statsAndLogging] psrfits_requantisation.cwl.requantise.requantize.cwl.stderr follows:
=========>
source: /.inject-apptainer-env.sh:354:11: invalid var name
Usage: psrfits_requantisation [options] [output tarball]
psrfits_requantisation: error: no such option: --output-sasid
<=========
[2026-05-13T19:37:12+0200] [Thread-9] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker CWLJob /project/ldv/Share/cache/tmp/tmppm_96yzg kind-CWLJob/instance-f7jiprcw.
[2026-05-13T19:37:12+0200] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-f7jiprcw v3
Exit reason: None
[2026-05-13T19:37:12+0200] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-f7jiprcw v5
[2026-05-13T19:37:12+0200] [MainThread] [W] [toil.leader] Log from job "kind-CWLJob/instance-f7jiprcw" follows:
=========>
[2026-05-13T19:36:22+0200] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
[2026-05-13T19:36:22+0200] [MainThread] [I] [toil] Running Toil version 9.1.2-355b72ba0e425619c0367562caf2a337078dba65 on host wn-la-12.spider.surfsara.nl.
[2026-05-13T19:36:22+0200] [MainThread] [I] [toil.worker] Working on job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-f7jiprcw v4
/project/ldv/Software/executor-venv-toil9/lib/python3.9/site-packages/pydantic/_internal/_generate_schema.py:2249: UnsupportedFieldAttributeWarning: The 'default' attribute with value None was provided to the `Field()` function, which has no effect in the context it was used. 'default' is field-specific metadata, and can only be attached to a model field using `Annotated` metadata or by assignment. This may have happened because an `Annotated` type alias using the `type` statement was used, or if the `Field()` function was attached to a single member of a union type.
warnings.warn(
[2026-05-13T19:36:23+0200] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-f7jiprcw v4) from description 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-f7jiprcw v4
[2026-05-13T19:36:24+0200] [MainThread] [W] [cwltool] You have specified '--preserve-entire-environment' while running a container which will override variables set in the container. This may break the container, be non-portable, and/or affect reproducibility.
[2026-05-13T19:36:24+0200] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run-test/workflows/psrfits_requantisation/workflow
[2026-05-13T19:37:11+0200] [MainThread] [I] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] /project/ldv/Share/cache/tmp/tmpywd4kp80$ singularity \
--quiet \
run \
--contain \
--ipc \
--cleanenv \
--no-eval \
--userns \
--home \
/project/ldv/Share/cache/tmp/tmpywd4kp80:/VNJAeE \
--mount=type=bind,source=/tmp/tmpw0ddyetf,target=/tmp \
--pwd \
/VNJAeE \
--net \
--network \
none \
/project/ldv/Share/run-test/workflows/psrfits_requantisation/workflow/git.astron.nl:5000_ldv_bf_double_tgz:latest.sif \
psrfits_requantisation \
L427020_SAP000_B000_S2_P014_bf.tar \
--output-sasid=102600000356
[2026-05-13T19:37:12+0200] [MainThread] [W] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] exited with status: 2
[2026-05-13T19:37:12+0200] [MainThread] [E] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] Job error:
("Error collecting output for parameter 'bf_archive': ../../../../workflows/psrfits_requantisation/steps/requantize.cwl:31:5: Did not find output file with glob pattern: ['102600000356_*.tar'].", {})
[2026-05-13T19:37:12+0200] [MainThread] [W] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] completed permanentFail
[2026-05-13T19:37:12+0200] [MainThread] [E] [toil.cwl.cwltoil] Failed command standard error:
source: /.inject-apptainer-env.sh:354:11: invalid var name
Usage: psrfits_requantisation [options] [output tarball]
psrfits_requantisation: error: no such option: --output-sasid
[2026-05-13T19:37:12+0200] [MainThread] [C] [toil.worker] Worker crashed with traceback:
Traceback (most recent call last):
File "/project/ldv/Software/executor-venv-toil9/lib/python3.9/site-packages/toil/worker.py", line 595, in workerScript
job._runner(
File "/project/ldv/Software/executor-venv-toil9/lib/python3.9/site-packages/toil/job.py", line 3254, in _runner
returnValues = self._run(jobGraph=None, fileStore=fileStore)
File "/project/ldv/Software/executor-venv-toil9/lib/python3.9/site-packages/toil/job.py", line 3137, in _run
return self.run(fileStore)
File "/project/ldv/Software/executor-venv-toil9/lib/python3.9/site-packages/toil/cwl/cwltoil.py", line 2847, in run
raise cwl_utils.errors.WorkflowException(status)
cwl_utils.errors.WorkflowException: permanentFail
[2026-05-13T19:37:12+0200] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host wn-la-12.spider.surfsara.nl
<=========
[2026-05-13T19:37:12+0200] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-f7jiprcw v5 with ID kind-CWLJob/instance-f7jiprcw to 2
[2026-05-13T19:37:12+0200] [MainThread] [I] [toil.leader] Issued job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-f7jiprcw v6 with job batch system ID: 8 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
srun: Job step aborted: Waiting up to 122 seconds for job step to finish.
[2026-05-13T19:37:57.187] error: *** JOB 35700276 ON wn-la-12 CANCELLED AT 2026-05-13T19:37:57 DUE to SIGNAL Terminated ***